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Clean/fresh Sierra install over working Sierra using clover

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What is the best way to approach a clean install of Sierra over an existing system? I've been searching all morning, but I haven't found anything clear.

Originally installed ML using Chimera. Updated to El Capitan w/clover. And again to Sierra. Everything right now works, USB 3.0, Handoff, iMessage, Appstore, etc...

I use this computer for development, so I use terminal to install random tools and libraries into the system. Along with all the other apps I've downloaded and removed over the years there seem to still be a lot of junk floating around the system. When I open Activity Monitor it appears though there are more than a few extra services running, and I'm always worried that something malicious is going on.

I remember it being a pain to get iMessage to work, generating serials, etc. Upgrading to Clover from Chimera was a headache as well, but once it was done every update afterwards worked smoothly. I would like to avoid the previous issues if possible. Some features were broken for months before I could figure out the issue.

Normally on my MacBook, I would backup the documents and files I want to transfer and then do a reinstall of the OS. Considering all the trouble I went through to get everything functioning on this machine before, is there a way to easily reinstall a clean Sierra system over the existing Sierra install on the same hard drive using the working Clover/EFI stuff? Or will I need to reinstall clover using the main method described on this site?
 
Carbon Copy Cloner [CCC] can be used to make an exact copy of your current disk to another for future restoration.
Disk Utility can be used to copy your current disk to another but CCC may be better.
 
Right, but the thing I would like to do is have a clean install of Sierra.

Everything works with Sierra right now, will use the same exact machine. I was hoping to keep the EFI and Clover settings to reinstall Sierra as if it was a brand new machine.
 
You can mount your EFI folder of your current good system [EFI contains all the sub folders and files including config.plist size:under 50MB] and copy and save it to a FD and copy and paste it back and replace that of a "clean install" when needed. You can use the EFI Mounter V3 or Clover Configurator to mount the EFI folder of your Current System Disk. Is that what you were looking for?
 
Right, but the thing I would like to do is have a clean install of Sierra.

Everything works with Sierra right now, will use the same exact machine. I was hoping to keep the EFI and Clover settings to reinstall Sierra as if it was a brand new machine.
You can actually format your hdd without deleting your EFI partition.
Just open disk utility and erase don't partition and your EFI will stay intact.

PS:That should be done with your unibeast installer of course.
 
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